I'm not really invested in the Windows vs Linux thing but config files in /etc never get silently changed or removed. If they are, it's a critical bug, although I've never really seen it happen.
If there are any updates to the service files, they'll be installed alongside the original file. For example, on Arch Linux, it'll be /etc/systemd/journald.conf.pacnew while the original journald.conf file will never be touched.